In southern China, it’s the season of “plum rains”, when wet weather helps the fruit ripen—but also causes severe flooding. This spring, China’s all-important housing market, which supports around a quarter of the economy and props up the price of commodities like iron ore and copper, is also looking leaky. Prices gains in top tier coastal markets weakened last month for the first time since January.

The ebbing of house price growth comes after two months of surprising buoyancy in the markets. Strong gains in February and...